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Archive for the ‘Lab Engine’ Category

MeSH, Publications and More

Sunday, May 10th, 2009

Aside from fixing bugs and making minor changes throughout Lab Engine, we’ve spent some time rethinking the Publications section:

Browse the MeSH terms in a 3D cloud

Browse the MeSH terms in an interactive 3D cloud

Firstly, publications are now automatically categorized by journals, which are listed on the right side. As a new feature, we’ve also added the ability to browse the publications’ MeSH tags in an interactive cloud format. The screenshot above doesn’t do it justice, I suggest you go check it out yourself in your Lab Engine account.

The Dashboard has also gotten an overhaul: it now automatically shows recent discussions, latest application results and a list of your open tasks. Should make it easier to see at a glance what’s been going on in your various projects.

For the full patch release notes, read after the break.

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Visualizing GenBank Sequences

Sunday, March 22nd, 2009

We’ve added another visualization tool that utilizes BioPython’s GenomeDiagram API to create graphs out of GenBank sequence files. A few examples:

ae017199

Circular graph

564

Linear graph

Currently it displays GC content and CDS features, and we’re seeking feedback on what other options to add.

Got a visualization tool you’d like to see simplified and integrated into Lab Engine? Then let me know in the comments.

Ramachandran Plot and more

Sunday, March 15th, 2009

It’s now possible to create beautiful Ramachandran plots with a single mouse-click from within Lab Engine. All you need is a PDB file, and you’re good to go. Below is a sample output for 1ATP:

As usual, there have been numerous minor improvements that you’ll notice as you go along. And if there’s an application/ visualization you would like to see integrated, let me know in the comments.

Import Publications by DOI or URL

Wednesday, March 4th, 2009

To make it even easier to manage your publications, it is now possible to add publications to your project using a DOI or URL. (thanks to Stew for the idea) Other changes in this minor patch include bug fixes, the ability to recover account information and email notifications on important activities.

Import publications by PMID, DOI or URL

Have any other feature requests or ideas you’d like to see? Then let me know in the comments!